Starting phenix.real_space_refine on Tue Mar 3 20:33:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7scg_25034/03_2026/7scg_25034.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scg_25034/03_2026/7scg_25034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7scg_25034/03_2026/7scg_25034.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scg_25034/03_2026/7scg_25034.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7scg_25034/03_2026/7scg_25034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scg_25034/03_2026/7scg_25034.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5460 2.51 5 N 1454 2.21 5 O 1561 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8539 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2547 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2158 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 10, 'TRANS': 272} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 2, 'ARG:plan': 4, 'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1675 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 8} Unresolved non-hydrogen planarities: 50 Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {'8RI': 1} Classifications: {'undetermined': 1, 'water': 2} Link IDs: {None: 2} Time building chain proxies: 2.08, per 1000 atoms: 0.24 Number of scatterers: 8539 At special positions: 0 Unit cell: (103.244, 122.332, 111.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1561 8.00 N 1454 7.00 C 5460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 217 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.54 Conformation dependent library (CDL) restraints added in 256.2 milliseconds 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 37.2% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 9 through 24 Processing helix chain 'B' and resid 29 through 33 Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 67 through 97 removed outlier: 4.002A pdb=" N VAL D 94 " --> pdb=" O MET D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 119 Processing helix chain 'D' and resid 120 through 131 removed outlier: 3.691A pdb=" N GLN D 124 " --> pdb=" O THR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 171 removed outlier: 3.845A pdb=" N CYS D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYS D 141 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE D 142 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE D 152 " --> pdb=" O TYR D 148 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 153 " --> pdb=" O TYR D 149 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.734A pdb=" N PHE D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 205 removed outlier: 3.621A pdb=" N TRP D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA D 197 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 224 through 241 Processing helix chain 'D' and resid 241 through 259 removed outlier: 3.653A pdb=" N VAL D 245 " --> pdb=" O PHE D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 261 No H-bonds generated for 'chain 'D' and resid 260 through 261' Processing helix chain 'D' and resid 262 through 266 removed outlier: 3.855A pdb=" N SER D 266 " --> pdb=" O ARG D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 304 Proline residue: D 295 - end of helix Processing helix chain 'D' and resid 311 through 337 removed outlier: 3.517A pdb=" N THR D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA D 323 " --> pdb=" O HIS D 319 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN D 328 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N SER D 329 " --> pdb=" O GLY D 325 " (cutoff:3.500A) Proline residue: D 333 - end of helix Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'A' and resid 8 through 31 removed outlier: 3.937A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.773A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.492A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.533A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.958A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 309 removed outlier: 4.196A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.733A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.755A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.635A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.659A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.097A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.692A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.850A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.548A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.763A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 206 through 210 removed outlier: 3.724A pdb=" N THR D 218 " --> pdb=" O THR D 207 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS D 209 " --> pdb=" O ASP D 216 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP D 216 " --> pdb=" O LYS D 209 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.913A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.502A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.502A pdb=" N THR E 118 " --> pdb=" O GLY E 10 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.379A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 142 through 147 removed outlier: 3.618A pdb=" N PHE E 200 " --> pdb=" O CYS E 147 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1351 1.31 - 1.44: 2431 1.44 - 1.56: 4842 1.56 - 1.69: 1 1.69 - 1.81: 91 Bond restraints: 8716 Sorted by residual: bond pdb=" C01 8RI D 401 " pdb=" N01 8RI D 401 " ideal model delta sigma weight residual 1.341 1.469 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C03 8RI D 401 " pdb=" C04 8RI D 401 " ideal model delta sigma weight residual 1.464 1.568 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C01 8RI D 401 " pdb=" C02 8RI D 401 " ideal model delta sigma weight residual 1.485 1.547 -0.062 2.00e-02 2.50e+03 9.55e+00 bond pdb=" C22 8RI D 401 " pdb=" O02 8RI D 401 " ideal model delta sigma weight residual 1.350 1.400 -0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" N SER B 74 " pdb=" CA SER B 74 " ideal model delta sigma weight residual 1.455 1.485 -0.031 1.32e-02 5.74e+03 5.42e+00 ... (remaining 8711 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 11562 1.63 - 3.25: 224 3.25 - 4.88: 43 4.88 - 6.50: 9 6.50 - 8.13: 4 Bond angle restraints: 11842 Sorted by residual: angle pdb=" C ASN D 150 " pdb=" CA ASN D 150 " pdb=" CB ASN D 150 " ideal model delta sigma weight residual 110.37 117.34 -6.97 1.78e+00 3.16e-01 1.53e+01 angle pdb=" N THR B 164 " pdb=" CA THR B 164 " pdb=" CB THR B 164 " ideal model delta sigma weight residual 114.17 109.91 4.26 1.14e+00 7.69e-01 1.39e+01 angle pdb=" N ASN D 150 " pdb=" CA ASN D 150 " pdb=" C ASN D 150 " ideal model delta sigma weight residual 113.02 109.14 3.88 1.20e+00 6.94e-01 1.05e+01 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.20 109.72 3.48 1.21e+00 6.83e-01 8.27e+00 angle pdb=" C THR B 29 " pdb=" N LEU B 30 " pdb=" CA LEU B 30 " ideal model delta sigma weight residual 121.54 126.98 -5.44 1.91e+00 2.74e-01 8.12e+00 ... (remaining 11837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 4684 17.70 - 35.40: 394 35.40 - 53.11: 52 53.11 - 70.81: 5 70.81 - 88.51: 4 Dihedral angle restraints: 5139 sinusoidal: 1883 harmonic: 3256 Sorted by residual: dihedral pdb=" CB CYS D 140 " pdb=" SG CYS D 140 " pdb=" SG CYS D 217 " pdb=" CB CYS D 217 " ideal model delta sinusoidal sigma weight residual 93.00 -179.48 -87.52 1 1.00e+01 1.00e-02 9.19e+01 dihedral pdb=" CA LEU B 95 " pdb=" C LEU B 95 " pdb=" N ARG B 96 " pdb=" CA ARG B 96 " ideal model delta harmonic sigma weight residual 180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 5136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1078 0.049 - 0.098: 239 0.098 - 0.147: 59 0.147 - 0.196: 2 0.196 - 0.245: 1 Chirality restraints: 1379 Sorted by residual: chirality pdb=" CA ASN D 150 " pdb=" N ASN D 150 " pdb=" C ASN D 150 " pdb=" CB ASN D 150 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA MET D 151 " pdb=" N MET D 151 " pdb=" C MET D 151 " pdb=" CB MET D 151 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 1376 not shown) Planarity restraints: 1486 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 149 " -0.015 2.00e-02 2.50e+03 3.02e-02 9.13e+00 pdb=" C TYR D 149 " 0.052 2.00e-02 2.50e+03 pdb=" O TYR D 149 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN D 150 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 164 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C THR B 164 " -0.030 2.00e-02 2.50e+03 pdb=" O THR B 164 " 0.011 2.00e-02 2.50e+03 pdb=" N THR B 165 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 200 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO D 201 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 201 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 201 " 0.022 5.00e-02 4.00e+02 ... (remaining 1483 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2214 2.80 - 3.32: 7517 3.32 - 3.85: 12922 3.85 - 4.37: 15157 4.37 - 4.90: 28551 Nonbonded interactions: 66361 Sorted by model distance: nonbonded pdb=" O SER E 52 " pdb=" NH1 ARG E 72 " model vdw 2.274 3.120 nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.280 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.286 3.040 nonbonded pdb=" OE2 GLU A 308 " pdb=" OG1 THR A 321 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR D 101 " pdb=" OD1 ASN D 104 " model vdw 2.304 3.040 ... (remaining 66356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.820 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 8719 Z= 0.224 Angle : 0.610 8.129 11848 Z= 0.340 Chirality : 0.043 0.245 1379 Planarity : 0.004 0.038 1486 Dihedral : 12.870 88.509 3028 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.26), residues: 1105 helix: 1.82 (0.28), residues: 371 sheet: -0.93 (0.31), residues: 294 loop : -1.41 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 98 TYR 0.011 0.002 TYR E 50 PHE 0.013 0.001 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 8716) covalent geometry : angle 0.60956 (11842) SS BOND : bond 0.00625 ( 3) SS BOND : angle 0.67504 ( 6) hydrogen bonds : bond 0.17825 ( 398) hydrogen bonds : angle 6.36831 ( 1128) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.311 Fit side-chains REVERT: B 247 ASP cc_start: 0.7577 (t0) cc_final: 0.7377 (t0) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.6305 time to fit residues: 77.1020 Evaluate side-chains 100 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.0040 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.146086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100611 restraints weight = 11014.191| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.29 r_work: 0.3171 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8719 Z= 0.105 Angle : 0.543 7.793 11848 Z= 0.282 Chirality : 0.042 0.150 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.637 34.491 1222 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.13 % Allowed : 7.55 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.26), residues: 1105 helix: 2.14 (0.28), residues: 371 sheet: -0.51 (0.30), residues: 296 loop : -1.25 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 251 TYR 0.019 0.001 TYR E 178 PHE 0.011 0.001 PHE A 189 TRP 0.017 0.001 TRP B 169 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8716) covalent geometry : angle 0.54265 (11842) SS BOND : bond 0.00536 ( 3) SS BOND : angle 0.54693 ( 6) hydrogen bonds : bond 0.04195 ( 398) hydrogen bonds : angle 4.35192 ( 1128) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.317 Fit side-chains REVERT: B 23 LYS cc_start: 0.8224 (tppt) cc_final: 0.7684 (tmmt) REVERT: B 247 ASP cc_start: 0.7896 (t0) cc_final: 0.7668 (t0) REVERT: D 243 MET cc_start: 0.7766 (ttp) cc_final: 0.7566 (ttt) REVERT: A 33 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8370 (tt0) REVERT: A 205 ARG cc_start: 0.7884 (pmt170) cc_final: 0.7481 (mmm160) outliers start: 10 outliers final: 2 residues processed: 126 average time/residue: 0.5761 time to fit residues: 76.9039 Evaluate side-chains 110 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 107 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 33 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 17 GLN B 75 GLN D 86 ASN D 109 ASN D 188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.093732 restraints weight = 10972.687| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.30 r_work: 0.3068 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 8719 Z= 0.218 Angle : 0.642 9.588 11848 Z= 0.329 Chirality : 0.045 0.158 1379 Planarity : 0.004 0.037 1486 Dihedral : 4.948 36.836 1222 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.59 % Allowed : 9.91 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.26), residues: 1105 helix: 2.19 (0.28), residues: 370 sheet: -0.30 (0.31), residues: 288 loop : -1.27 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 98 TYR 0.015 0.002 TYR B 105 PHE 0.015 0.001 PHE B 151 TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 8716) covalent geometry : angle 0.64247 (11842) SS BOND : bond 0.00687 ( 3) SS BOND : angle 0.63668 ( 6) hydrogen bonds : bond 0.05501 ( 398) hydrogen bonds : angle 4.41784 ( 1128) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.328 Fit side-chains REVERT: A 205 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7672 (mmm160) outliers start: 23 outliers final: 8 residues processed: 114 average time/residue: 0.5887 time to fit residues: 71.0172 Evaluate side-chains 112 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 205 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 68 optimal weight: 0.0270 chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 109 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.145779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100083 restraints weight = 11119.264| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.30 r_work: 0.3174 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8719 Z= 0.106 Angle : 0.518 6.622 11848 Z= 0.271 Chirality : 0.041 0.151 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.477 33.969 1222 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.36 % Allowed : 12.39 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.26), residues: 1105 helix: 2.40 (0.28), residues: 371 sheet: -0.10 (0.31), residues: 278 loop : -1.13 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 98 TYR 0.016 0.001 TYR E 178 PHE 0.011 0.001 PHE A 189 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 8716) covalent geometry : angle 0.51758 (11842) SS BOND : bond 0.00480 ( 3) SS BOND : angle 0.63586 ( 6) hydrogen bonds : bond 0.04056 ( 398) hydrogen bonds : angle 4.07944 ( 1128) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.311 Fit side-chains REVERT: A 205 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7692 (mmm160) outliers start: 21 outliers final: 9 residues processed: 121 average time/residue: 0.5873 time to fit residues: 75.3093 Evaluate side-chains 117 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 205 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 52 optimal weight: 50.0000 chunk 45 optimal weight: 0.2980 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 88 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 81 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 109 ASN A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.135111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.090276 restraints weight = 10826.712| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.29 r_work: 0.3085 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 8719 Z= 0.251 Angle : 0.674 10.399 11848 Z= 0.344 Chirality : 0.046 0.156 1379 Planarity : 0.004 0.039 1486 Dihedral : 5.079 37.950 1222 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.38 % Allowed : 13.06 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.25), residues: 1105 helix: 2.26 (0.27), residues: 370 sheet: -0.18 (0.30), residues: 290 loop : -1.20 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 98 TYR 0.019 0.002 TYR B 105 PHE 0.015 0.002 PHE B 151 TRP 0.016 0.002 TRP B 82 HIS 0.007 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00633 ( 8716) covalent geometry : angle 0.67376 (11842) SS BOND : bond 0.00708 ( 3) SS BOND : angle 0.77429 ( 6) hydrogen bonds : bond 0.05809 ( 398) hydrogen bonds : angle 4.37006 ( 1128) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 102 time to evaluate : 0.345 Fit side-chains REVERT: B 153 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.8119 (m-30) REVERT: B 327 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8656 (t) outliers start: 30 outliers final: 12 residues processed: 120 average time/residue: 0.5606 time to fit residues: 71.4498 Evaluate side-chains 116 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 276 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 109 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.139659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.095488 restraints weight = 10760.742| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.29 r_work: 0.3164 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8719 Z= 0.109 Angle : 0.521 6.526 11848 Z= 0.273 Chirality : 0.041 0.150 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.473 34.703 1222 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.14 % Allowed : 14.75 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.26), residues: 1105 helix: 2.47 (0.28), residues: 372 sheet: 0.09 (0.31), residues: 278 loop : -1.08 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 98 TYR 0.015 0.001 TYR E 178 PHE 0.011 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 8716) covalent geometry : angle 0.52137 (11842) SS BOND : bond 0.00512 ( 3) SS BOND : angle 0.72273 ( 6) hydrogen bonds : bond 0.04065 ( 398) hydrogen bonds : angle 4.02518 ( 1128) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.321 Fit side-chains REVERT: A 205 ARG cc_start: 0.7878 (mtm110) cc_final: 0.7597 (mpp-170) REVERT: A 309 ASP cc_start: 0.8034 (p0) cc_final: 0.7822 (p0) outliers start: 19 outliers final: 13 residues processed: 125 average time/residue: 0.5526 time to fit residues: 73.3987 Evaluate side-chains 123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 102 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 88 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN D 109 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.137224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092482 restraints weight = 10889.261| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.30 r_work: 0.3118 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8719 Z= 0.174 Angle : 0.590 8.180 11848 Z= 0.304 Chirality : 0.043 0.150 1379 Planarity : 0.004 0.036 1486 Dihedral : 4.701 35.320 1222 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.04 % Allowed : 15.20 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.26), residues: 1105 helix: 2.43 (0.27), residues: 374 sheet: 0.05 (0.31), residues: 280 loop : -1.13 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 277 TYR 0.014 0.001 TYR E 178 PHE 0.013 0.001 PHE B 241 TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 8716) covalent geometry : angle 0.59009 (11842) SS BOND : bond 0.00627 ( 3) SS BOND : angle 0.66908 ( 6) hydrogen bonds : bond 0.04907 ( 398) hydrogen bonds : angle 4.12703 ( 1128) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.241 Fit side-chains REVERT: B 70 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8915 (pt) REVERT: B 117 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9110 (mp) REVERT: B 153 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7965 (m-30) REVERT: B 327 VAL cc_start: 0.8892 (OUTLIER) cc_final: 0.8644 (t) REVERT: E 51 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8427 (tp) outliers start: 27 outliers final: 12 residues processed: 123 average time/residue: 0.5422 time to fit residues: 70.8939 Evaluate side-chains 124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 0.0970 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 17 GLN D 109 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.146160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100286 restraints weight = 10967.854| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.29 r_work: 0.3177 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8719 Z= 0.102 Angle : 0.507 6.285 11848 Z= 0.266 Chirality : 0.041 0.150 1379 Planarity : 0.003 0.033 1486 Dihedral : 4.302 31.818 1222 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.48 % Allowed : 16.33 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.26), residues: 1105 helix: 2.66 (0.27), residues: 369 sheet: 0.04 (0.30), residues: 295 loop : -1.07 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 277 TYR 0.015 0.001 TYR E 178 PHE 0.011 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8716) covalent geometry : angle 0.50682 (11842) SS BOND : bond 0.00423 ( 3) SS BOND : angle 0.58378 ( 6) hydrogen bonds : bond 0.03844 ( 398) hydrogen bonds : angle 3.92861 ( 1128) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.315 Fit side-chains REVERT: B 262 MET cc_start: 0.9255 (tpp) cc_final: 0.9008 (ttm) REVERT: E 51 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8341 (tp) outliers start: 22 outliers final: 11 residues processed: 129 average time/residue: 0.5355 time to fit residues: 73.5596 Evaluate side-chains 125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain E residue 51 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 66 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 51 optimal weight: 0.0010 chunk 85 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 0.0040 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN B 17 GLN D 109 ASN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN A 294 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.148727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103291 restraints weight = 11009.423| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.30 r_work: 0.3177 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8719 Z= 0.089 Angle : 0.481 5.971 11848 Z= 0.252 Chirality : 0.040 0.151 1379 Planarity : 0.003 0.032 1486 Dihedral : 3.965 26.956 1222 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.14 % Allowed : 16.44 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.26), residues: 1105 helix: 2.78 (0.27), residues: 369 sheet: 0.03 (0.30), residues: 308 loop : -0.94 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 277 TYR 0.014 0.001 TYR E 178 PHE 0.011 0.001 PHE A 189 TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 8716) covalent geometry : angle 0.48064 (11842) SS BOND : bond 0.00382 ( 3) SS BOND : angle 0.57756 ( 6) hydrogen bonds : bond 0.03368 ( 398) hydrogen bonds : angle 3.76413 ( 1128) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.248 Fit side-chains REVERT: B 247 ASP cc_start: 0.7704 (t0) cc_final: 0.7450 (t0) REVERT: B 284 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8089 (mt) REVERT: A 182 THR cc_start: 0.7259 (p) cc_final: 0.6951 (t) REVERT: A 247 MET cc_start: 0.8398 (mtt) cc_final: 0.8186 (mtm) outliers start: 19 outliers final: 10 residues processed: 132 average time/residue: 0.5343 time to fit residues: 75.0865 Evaluate side-chains 124 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 3 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.145832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.099585 restraints weight = 10994.569| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.30 r_work: 0.3175 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8719 Z= 0.122 Angle : 0.529 6.554 11848 Z= 0.276 Chirality : 0.041 0.151 1379 Planarity : 0.003 0.034 1486 Dihedral : 4.178 27.450 1222 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.58 % Allowed : 17.68 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.26), residues: 1105 helix: 2.81 (0.27), residues: 368 sheet: 0.07 (0.30), residues: 302 loop : -0.99 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 277 TYR 0.014 0.001 TYR E 178 PHE 0.011 0.001 PHE B 241 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 8716) covalent geometry : angle 0.52893 (11842) SS BOND : bond 0.00500 ( 3) SS BOND : angle 0.60302 ( 6) hydrogen bonds : bond 0.04010 ( 398) hydrogen bonds : angle 3.89396 ( 1128) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2210 Ramachandran restraints generated. 1105 Oldfield, 0 Emsley, 1105 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.213 Fit side-chains REVERT: A 182 THR cc_start: 0.7327 (p) cc_final: 0.7040 (t) outliers start: 14 outliers final: 10 residues processed: 120 average time/residue: 0.5499 time to fit residues: 70.0884 Evaluate side-chains 120 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 57 SER Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain A residue 21 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 58 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 55 optimal weight: 0.0670 chunk 52 optimal weight: 0.1980 chunk 104 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 76 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.148098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.102437 restraints weight = 10990.851| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.29 r_work: 0.3215 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8719 Z= 0.094 Angle : 0.488 6.175 11848 Z= 0.257 Chirality : 0.041 0.151 1379 Planarity : 0.003 0.032 1486 Dihedral : 3.953 24.777 1222 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.80 % Allowed : 17.12 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.26), residues: 1105 helix: 2.84 (0.27), residues: 369 sheet: 0.09 (0.30), residues: 303 loop : -0.93 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 277 TYR 0.014 0.001 TYR E 178 PHE 0.010 0.001 PHE A 189 TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 8716) covalent geometry : angle 0.48826 (11842) SS BOND : bond 0.00400 ( 3) SS BOND : angle 0.61705 ( 6) hydrogen bonds : bond 0.03438 ( 398) hydrogen bonds : angle 3.81106 ( 1128) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2878.78 seconds wall clock time: 49 minutes 42.04 seconds (2982.04 seconds total)